Today, my Let's Encrypt certificate was renewed but the site folder was changed back to default (public_html). When I installed Vesta, I've changed it to public_shtml. Is it possible to configure it to not change after each renewing?

I have the same issue. Basically, every time certificates are renewed, conf/web/domain.tld.apache.ssl.conf files are reset to default. Is there a way where we can override the default config for each domain set by let's encrypt on certificate renewal?